TAIR is pleased to announce the Single Nucleotide Polymorphisms (SNPs)
table at
http://arabidopsis.org/SNPs.html.
This first set of SNPs was generously provided to us by Dr. Michael
Mindrinos and includes the entire set of 412 SNPs described in Cho et
al., Nat Genet 1999 Oct. 23(2):203-7. These SNPs have been given the
additional prefix SGC- for the Stanford Genome Center. New SNPs will be
added and given contributor-specific prefixes.
THe sequences shown in the table have been confirmed by sequencing and
HPLC to be polymorphic between the Col and Ler ecotypes. A subset of the
SNPs that have been experimentally shown to distinguish between Col and
Ler on oligonucleotide arrays are indicated by asterisks. Using BLAST we
have located 286 of the SNPs to AGI clones on the TAIR sequence map
(http://arabidopsis.org/cgi-bin/maps/Schrom) and sequence table
(http://arabidopsis.org/cgi-bin/maps/Seqtable.pl).
RI map positions for many of the SNPs will also be available shortly.
The utility of the SNPs as markers may also be extended. Approximately
30% of the SNPs should contain restriction site polymorphisms that can be
used to develop CAPs markers. We will update the table with data on the
restriction sites soon. Some polymorphic regions are deletions/insertions
that may be useful in designing SSLP primers.
Please let us know if you develop any of these SNPs into markers and we
will update our Marker table.
Please send your comments and questions to curator at arabidopsis.org
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Leonore Reiser lreiser at stanford.edu
The Arabidopsis Information Resource FAX: (650) 325-6857
Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
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